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Magnesium in PDB 4ii3: Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg

Enzymatic activity of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg

All present enzymatic activity of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg, PDB code: 4ii3 was solved by S.K.Olsen, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.500, 113.300, 126.600, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.3

Other elements in 4ii3:

The structure of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg (pdb code 4ii3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg, PDB code: 4ii3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ii3

Go back to Magnesium Binding Sites List in 4ii3
Magnesium binding site 1 out of 4 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:2.8
occ:1.00
 O2B A:ATP1103 2.3 61.7 1.0
O2A A:ATP1103 2.4 50.4 1.0
O A:HOH1226 2.6 13.4 1.0
OD2 A:ASP537 2.6 41.4 1.0
O1G A:ATP1103 2.7 58.4 1.0
O A:HOH1263 2.7 28.3 1.0
O A:HOH1246 3.1 24.6 1.0
CB A:ASP537 3.1 41.7 1.0
CG A:ASP537 3.1 41.2 1.0
PB A:ATP1103 3.3 62.6 1.0
PA A:ATP1103 3.4 51.9 1.0
O3B A:ATP1103 3.5 60.6 1.0
O3A A:ATP1103 3.6 58.2 1.0
PG A:ATP1103 3.7 59.5 1.0
O5' A:ATP1103 4.0 51.2 1.0
OD1 A:ASP537 4.2 41.0 1.0
O A:HOH1259 4.5 22.0 1.0
CA A:ASP537 4.6 40.9 1.0
O2G A:ATP1103 4.7 59.2 1.0
O3G A:ATP1103 4.7 58.5 1.0
O1B A:ATP1103 4.7 60.1 1.0
O1A A:ATP1103 4.8 49.4 1.0
O B:GLY76 4.9 53.8 1.0
O A:ASP537 5.0 41.6 1.0

Magnesium binding site 2 out of 4 in 4ii3

Go back to Magnesium Binding Sites List in 4ii3
Magnesium binding site 2 out of 4 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:28.4
occ:1.00
 OE2 A:GLU468 2.7 78.5 1.0
OD2 A:ASP465 2.7 56.7 1.0
O1B A:ATP1103 2.9 60.1 1.0
O2G A:ATP1103 3.2 59.2 1.0
O A:HOH1212 3.4 30.1 1.0
CD A:GLU468 3.5 77.2 1.0
CG A:ASP465 3.6 56.6 1.0
PB A:ATP1103 3.8 62.6 1.0
OE1 A:GLU468 3.8 79.3 1.0
OD1 A:ASP465 3.8 57.8 1.0
O2B A:ATP1103 3.8 61.7 1.0
O A:HOH1259 4.0 22.0 1.0
O3B A:ATP1103 4.3 60.6 1.0
PG A:ATP1103 4.4 59.5 1.0
OD1 A:ASN471 4.5 57.3 1.0
CG A:GLU468 4.7 72.7 1.0
CB A:ASP465 4.9 54.6 1.0
O1G A:ATP1103 4.9 58.4 1.0
ND2 A:ASN471 5.0 57.2 1.0
O A:HOH1263 5.0 28.3 1.0
O A:SER466 5.0 57.9 1.0

Magnesium binding site 3 out of 4 in 4ii3

Go back to Magnesium Binding Sites List in 4ii3
Magnesium binding site 3 out of 4 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:42.5
occ:1.00
 O2B C:ATP1103 2.7 82.1 1.0
O C:HOH1213 2.7 32.8 1.0
O2A C:ATP1103 2.7 70.5 1.0
OD2 C:ASP537 3.1 49.2 1.0
O3B C:ATP1103 3.2 83.9 1.0
O3G C:ATP1103 3.3 83.0 1.0
PB C:ATP1103 3.4 84.4 1.0
CB C:ASP537 3.5 45.4 1.0
CG C:ASP537 3.6 48.3 1.0
PG C:ATP1103 3.6 84.2 1.0
O2G C:ATP1103 3.8 82.6 1.0
PA C:ATP1103 3.8 71.7 1.0
O3A C:ATP1103 4.0 78.3 1.0
OD1 C:ASP537 4.6 49.2 1.0
CG2 C:VAL852 4.8 54.0 1.0
O1B C:ATP1103 4.9 82.0 1.0
O1A C:ATP1103 4.9 70.0 1.0
CA C:ASP537 4.9 43.4 1.0
C5' C:ATP1103 5.0 59.3 1.0
O5' C:ATP1103 5.0 65.2 1.0

Magnesium binding site 4 out of 4 in 4ii3

Go back to Magnesium Binding Sites List in 4ii3
Magnesium binding site 4 out of 4 in the Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of S. Pombe Ubiquitin Activating Enzyme 1 (UBA1) in Complex with Ubiquitin and Atp/Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:29.2
occ:1.00
 OE2 C:GLU468 2.6 81.2 1.0
O1G C:ATP1103 3.0 83.2 1.0
O1B C:ATP1103 3.1 82.0 1.0
OD2 C:ASP465 3.2 59.1 1.0
O3G C:ATP1103 3.3 83.0 1.0
CD C:GLU468 3.4 80.2 1.0
OE1 C:GLU468 3.5 82.2 1.0
PG C:ATP1103 3.6 84.2 1.0
PB C:ATP1103 3.9 84.4 1.0
CG C:ASP465 4.0 61.1 1.0
O3B C:ATP1103 4.1 83.9 1.0
O2B C:ATP1103 4.1 82.1 1.0
OD1 C:ASP465 4.2 61.1 1.0
OD1 C:ASN471 4.5 69.6 1.0
NZ C:LYS812 4.5 75.1 1.0
CG C:GLU468 4.7 76.1 1.0
OD2 C:ASP813 4.7 75.1 1.0
ND2 C:ASN471 4.7 69.8 1.0

Reference:

S.K.Olsen, C.D.Lima. Structure of A Ubiquitin E1-E2 Complex: Insights to E1-E2 Thioester Transfer. Mol.Cell V. 49 884 2013.
ISSN: ISSN 1097-2765
PubMed: 23416107
DOI: 10.1016/J.MOLCEL.2013.01.013
Page generated: Mon Aug 11 14:12:04 2025

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